From fcd74ef4b60e62813837fb893d5557a52e21a2c3 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed, 29 Jan 2020 10:02:03 +0530
Subject: [PATCH 01/21] python2 is EOL. Upgrading to python3. Probably this is
 the reason behind

---
 moose-nightly.rb | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/moose-nightly.rb b/moose-nightly.rb
index 67bcdcd..5ae2036 100644
--- a/moose-nightly.rb
+++ b/moose-nightly.rb
@@ -1,12 +1,12 @@
 class MooseNightly < Formula
   desc "Multiscale Object Oriented Simulation Environment"
   homepage "http://moose.ncbs.res.in"
-  head "https://github.com/BhallaLab/moose-core.git", :branch => "chhennapoda"
+  head "https://github.com/BhallaLab/moose-core.git", :branch => "master"
 
   depends_on "cmake" => :build
   depends_on "gsl"
-  depends_on :python if MacOS.version <= :snow_leopard
   depends_on "numpy"
+  depends_on "python@3" if MacOS.version <= :snow_leopard
 
   def install
     (buildpath/"VERSION").write("#{version}\n")
@@ -15,19 +15,19 @@ def install
     mkdir "_build" do
       system "cmake", "..", *args
       system "make"
-      system "make install"
+      system "make", "install"
     end
   end
 
   def caveats; <<-EOS
     Please also install the following using pip
-      $ pip install matplotlib networkx 
+      $ pip install matplotlib networkx
     Optionally, you can install the folllowing for sbml and NeuroML support.
       $ pip install python-libsbml pyNeuroML
-    EOS
+  EOS
   end
 
   test do
-    system "python", "-c", "import moose;print(moose.__file__)"
+    system "python3", "-c", "import moose;print(moose.__file__, moose.__version__)"
   end
 end

From 69d866f3e3a792ac760dade751127b84358a686f Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed, 29 Jan 2020 10:38:23 +0530
Subject: [PATCH 02/21] Updating to python3.

---
 moose.rb | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/moose.rb b/moose.rb
index 4e6c386..66597d2 100644
--- a/moose.rb
+++ b/moose.rb
@@ -7,28 +7,29 @@ class Moose < Formula
 
   depends_on "cmake" => :build
   depends_on "gsl"
-  depends_on :python if MacOS.version <= :snow_leopard
   depends_on "numpy"
+  depends_on "python" 
 
   def install
     args = std_cmake_args
     args << "-DCMAKE_SKIP_RPATH=ON"
+    args << "-DPYTHON_EXECUTABLE=/usr/local/bin/python3"
     args << "-DVERSION_MOOSE=#{version}"
     mkdir "_build" do
       system "cmake", "..", *args
-      system "make install"
+      system "make", "install"
     end
   end
 
   def caveats; <<-EOS
     Please also install the following using pip
-      $ pip install matplotlib networkx 
+      $ pip install matplotlib networkx
      Optionally, you can install the folllowing for sbml and NeuroML support.
       $ pip install python-libsbml pyNeuroML
-    EOS
+  EOS
   end
 
   test do
-    system "python", "-c", "import moose; print( moose.__version__) "
+    system "python3", "-c", "import moose; print(moose.__file__, moose.__version__)"
   end
 end

From 4a3c8d36bffb0c0082021082cce66c0c7d7842f7 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Wed, 29 Jan 2020 10:39:38 +0530
Subject: [PATCH 03/21] Time to update chamcham branch.

---
 moose-nightly.rb | 2 +-
 moose.rb         | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/moose-nightly.rb b/moose-nightly.rb
index 5ae2036..3d7e3bb 100644
--- a/moose-nightly.rb
+++ b/moose-nightly.rb
@@ -6,7 +6,7 @@ class MooseNightly < Formula
   depends_on "cmake" => :build
   depends_on "gsl"
   depends_on "numpy"
-  depends_on "python@3" if MacOS.version <= :snow_leopard
+  depends_on "python"
 
   def install
     (buildpath/"VERSION").write("#{version}\n")
diff --git a/moose.rb b/moose.rb
index 66597d2..621844c 100644
--- a/moose.rb
+++ b/moose.rb
@@ -13,7 +13,6 @@ class Moose < Formula
   def install
     args = std_cmake_args
     args << "-DCMAKE_SKIP_RPATH=ON"
-    args << "-DPYTHON_EXECUTABLE=/usr/local/bin/python3"
     args << "-DVERSION_MOOSE=#{version}"
     mkdir "_build" do
       system "cmake", "..", *args

From 69f42e2213323db90f48db44b607697c3ffd6d54 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Fri, 31 Jan 2020 12:21:24 +0530
Subject: [PATCH 04/21] Builds locally

---
 moose-nightly.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/moose-nightly.rb b/moose-nightly.rb
index 3d7e3bb..7b4f5c8 100644
--- a/moose-nightly.rb
+++ b/moose-nightly.rb
@@ -1,7 +1,7 @@
 class MooseNightly < Formula
   desc "Multiscale Object Oriented Simulation Environment"
   homepage "http://moose.ncbs.res.in"
-  head "https://github.com/BhallaLab/moose-core.git", :branch => "master"
+  head "https://github.com/dilawar/moose-core.git", :branch => "master"
 
   depends_on "cmake" => :build
   depends_on "gsl"

From 304b06123891e3cfd4257912bb0eb76a09157d01 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Fri, 31 Jan 2020 12:56:35 +0530
Subject: [PATCH 05/21] v3.1.5rc1

---
 moose.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/moose.rb b/moose.rb
index 621844c..8c601a1 100644
--- a/moose.rb
+++ b/moose.rb
@@ -1,9 +1,9 @@
 class Moose < Formula
   desc "Multiscale Object Oriented Simulation Environment"
   homepage "http://moose.ncbs.res.in"
-  url "https://github.com/BhallaLab/moose-core/archive/v3.1.4.tar.gz"
-  sha256 "5d8e56e4361723fc30598d87fecfeab67be471abc0bc017a334357fa2160cc1a"
-  head "https://github.com/BhallaLab/moose-core.git", :branch=>"chamcham"
+  url "https://github.com/dilawar/moose-core/archive/v3.1.5rc1.tar.gz"
+  sha256 "74d8ca49662e28e3742f520ff1017ba520e2d1f9e1f94f4361c85066c1fb17e6"
+  head "https://github.com/dilawar/moose-core.git", :branch=>"chamcham"
 
   depends_on "cmake" => :build
   depends_on "gsl"

From d561d7888a3eb14f307510b734df99110ea5ae42 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 09:19:31 +0530
Subject: [PATCH 06/21] Seems like it worked #1.

---
 moose.rb | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/moose.rb b/moose.rb
index 8c601a1..57808ac 100644
--- a/moose.rb
+++ b/moose.rb
@@ -8,7 +8,7 @@ class Moose < Formula
   depends_on "cmake" => :build
   depends_on "gsl"
   depends_on "numpy"
-  depends_on "python" 
+  depends_on "python@3" 
 
   def install
     args = std_cmake_args
@@ -16,7 +16,12 @@ def install
     args << "-DVERSION_MOOSE=#{version}"
     mkdir "_build" do
       system "cmake", "..", *args
-      system "make", "install"
+      system "make"
+      # NOTE: https://github.com/Homebrew/brew/blob/master/docs/Python-for-Formula-Authors.md
+      cd "python" do
+        system "cp", "setup.cmake.py", "setup.py"
+        system "python3", *Language::Python.setup_install_args(prefix)
+      end
     end
   end
 
@@ -29,6 +34,6 @@ def caveats; <<-EOS
   end
 
   test do
-    system "python3", "-c", "import moose; print(moose.__file__, moose.__version__)"
+    system "python@3", "-c", "import moose; print(moose.__file__, moose.__version__)"
   end
 end

From f124f930cb364472eb0445ed20f98a85317719f3 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 09:30:05 +0530
Subject: [PATCH 07/21] Both formulae are fixed (hopefully. Time to test on
 OSX) #1.

---
 moose-nightly.rb | 15 ++++++++++-----
 moose.rb         |  8 ++++----
 2 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/moose-nightly.rb b/moose-nightly.rb
index 7b4f5c8..e999f75 100644
--- a/moose-nightly.rb
+++ b/moose-nightly.rb
@@ -1,6 +1,7 @@
 class MooseNightly < Formula
   desc "Multiscale Object Oriented Simulation Environment"
   homepage "http://moose.ncbs.res.in"
+  version "3.2-nightly"
   head "https://github.com/dilawar/moose-core.git", :branch => "master"
 
   depends_on "cmake" => :build
@@ -15,15 +16,19 @@ def install
     mkdir "_build" do
       system "cmake", "..", *args
       system "make"
-      system "make", "install"
+      # NOTE: https://github.com/Homebrew/brew/blob/master/docs/Python-for-Formula-Authors.md
+      cd "python" do
+        system "cp", "setup.cmake.py", "setup.py"
+        system "python3", *Language::Python.setup_install_args(prefix)
+      end
     end
   end
 
   def caveats; <<-EOS
-    Please also install the following using pip
-      $ pip install matplotlib networkx
-    Optionally, you can install the folllowing for sbml and NeuroML support.
-      $ pip install python-libsbml pyNeuroML
+    Please install the following as well,
+      $ python3 -m pip install matplotlib networkx
+    And optionally, folllowing are needed for SBML and NeuroML.
+      $ python3 -m pip install python-libsbml pyNeuroML
   EOS
   end
 
diff --git a/moose.rb b/moose.rb
index 57808ac..1796af2 100644
--- a/moose.rb
+++ b/moose.rb
@@ -26,10 +26,10 @@ def install
   end
 
   def caveats; <<-EOS
-    Please also install the following using pip
-      $ pip install matplotlib networkx
-     Optionally, you can install the folllowing for sbml and NeuroML support.
-      $ pip install python-libsbml pyNeuroML
+    Please install the following as well,
+      $ python3 -m pip install matplotlib networkx
+    And optionally, folllowing are needed for SBML and NeuroML.
+      $ python3 -m pip install python-libsbml pyNeuroML
   EOS
   end
 

From c7d301097dfc4e17a6cc7a728e767d731f42fd63 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 09:33:35 +0530
Subject: [PATCH 08/21] Added travis script.

---
 .travis.yml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..b2bacb5
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,24 @@
+language: cpp
+sudo: required
+
+os:
+- osx
+
+notifications:
+  email:
+    recipients:
+    - dilawar.s.rajput@gmail.com
+    on_success: change
+    on_failure: always
+
+before_script:
+- nvm get head 
+
+script:
+  - brew tap dilawar/moose
+  - brew install moose
+  - python3 -c "import moose; print(dir(moose))"
+  - brew uninstall -f moose 
+  - brew install --HEAD moose-nightly
+  - python3 -c "import moose; print(dir(moose))"
+  - set +e

From 8e86618a1ba56c5b59bcc0d9f1dd5307998714d3 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 09:34:12 +0530
Subject: [PATCH 09/21] Minor tweaks in readme file.

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index aff9540..3493349 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,5 @@
 # homebrew-moose
+
 Homebrew formulae for MOOSE and related projects
 
 # Install MOOSE

From 72a9294c9df7900d4413b3c9ff52e42c50c2c39e Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 09:35:41 +0530
Subject: [PATCH 10/21] Removed nvm command from travis script.

---
 .travis.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index b2bacb5..bab916a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,9 +11,6 @@ notifications:
     on_success: change
     on_failure: always
 
-before_script:
-- nvm get head 
-
 script:
   - brew tap dilawar/moose
   - brew install moose

From 56134be97c432a53ea8550abd7fb6494d09edffc Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Sat, 1 Feb 2020 09:39:41 +0530
Subject: [PATCH 11/21] Update README.md

---
 README.md | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 3493349..c2e3887 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,8 @@
-# homebrew-moose
-
 Homebrew formulae for MOOSE and related projects
 
-# Install MOOSE
-
-    $ brew tap BhallaLab/moose
-    $ brew install moose 
+# Installation
 
 
+    $ brew tap BhallaLab/moose
+    $ brew install moose                  # For stable version.
+    $ brew install --HEAD moose-nightly   # for bleeding edge version

From c6fea958793de959ce7b3368a82bcbdffd212c60 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 09:47:01 +0530
Subject: [PATCH 12/21] Force python3.

---
 .travis.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index bab916a..4f5b9d0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,7 +2,7 @@ language: cpp
 sudo: required
 
 os:
-- osx
+  - osx
 
 notifications:
   email:
@@ -12,6 +12,8 @@ notifications:
     on_failure: always
 
 script:
+  - brew install python
+  - brew link --overwrite python
   - brew tap dilawar/moose
   - brew install moose
   - python3 -c "import moose; print(dir(moose))"

From e6ca625948d2e0dd7fe877ddb2aabd59bc42bdc1 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 09:47:24 +0530
Subject: [PATCH 13/21] Force overwrite python3.

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 4f5b9d0..c2e497b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -12,8 +12,8 @@ notifications:
     on_failure: always
 
 script:
-  - brew install python
-  - brew link --overwrite python
+  - brew install python@3
+  - brew link --overwrite python@3
   - brew tap dilawar/moose
   - brew install moose
   - python3 -c "import moose; print(dir(moose))"

From 709947949a0744fdb7bbdf1b3d6b482115320673 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 14:13:56 +0530
Subject: [PATCH 14/21] Use newer OSX images. Default is 9.x. Now using 10.x
 and 11.x

---
 .travis.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index c2e497b..eb821f4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,6 +4,10 @@ sudo: required
 os:
   - osx
 
+oxs_image:
+  - xcode11.3
+  - xcode10.3
+
 notifications:
   email:
     recipients:

From 213a451b4ede02de045b4e4075bcfd8d5785dc53 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 14:31:17 +0530
Subject: [PATCH 15/21] Using absolute paths.

---
 .travis.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index eb821f4..a5f97fc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -20,8 +20,6 @@ script:
   - brew link --overwrite python@3
   - brew tap dilawar/moose
   - brew install moose
-  - python3 -c "import moose; print(dir(moose))"
-  - brew uninstall -f moose 
   - brew install --HEAD moose-nightly
-  - python3 -c "import moose; print(dir(moose))"
+  - /usr/local/bin/python3 -c "import moose; print(dir(moose))"
   - set +e

From d8d272a9abd5f87ee94050e8c9757d61b373a1dd Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 14:48:08 +0530
Subject: [PATCH 16/21] Some minor tweaks to test if this works.

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a5f97fc..efa8827 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -16,8 +16,9 @@ notifications:
     on_failure: always
 
 script:
+  - brew unlink python@2
   - brew install python@3
-  - brew link --overwrite python@3
+  - brew link --overwrite python
   - brew tap dilawar/moose
   - brew install moose
   - brew install --HEAD moose-nightly

From 2ed8d4f7cd7d29ed8f7c306d57fe1129b90d804f Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 14:55:23 +0530
Subject: [PATCH 17/21] Added flag to travis build. When building moose, be
 verbose.

---
 .travis.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index efa8827..1ccbeb4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -21,6 +21,5 @@ script:
   - brew link --overwrite python
   - brew tap dilawar/moose
   - brew install moose
-  - brew install --HEAD moose-nightly
+  - brew install -v --HEAD moose-nightly
   - /usr/local/bin/python3 -c "import moose; print(dir(moose))"
-  - set +e

From a70fce10f2c6ef76a4f7755061a18b7700496e16 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 19:52:41 +0530
Subject: [PATCH 18/21] Adding traps in travis. We only care for errors in our
 setup.

---
 .travis.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 1ccbeb4..cb7686e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -16,10 +16,13 @@ notifications:
     on_failure: always
 
 script:
+  - set +e
   - brew unlink python@2
   - brew install python@3
   - brew link --overwrite python
+  - set -e
   - brew tap dilawar/moose
   - brew install moose
   - brew install -v --HEAD moose-nightly
   - /usr/local/bin/python3 -c "import moose; print(dir(moose))"
+  - set +e

From ea2a03d532ecb539262b54c1d9867b56d57cc243 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Sat, 1 Feb 2020 20:00:36 +0530
Subject: [PATCH 19/21] Adding more tests.

---
 .travis.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index cb7686e..aa47225 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -17,8 +17,9 @@ notifications:
 
 script:
   - set +e
+  - export PATH=/usr/local/bin:$PATH
   - brew unlink python@2
-  - brew install python@3
+  - brew install python@3 graphviz
   - brew link --overwrite python
   - set -e
   - brew tap dilawar/moose
@@ -26,3 +27,5 @@ script:
   - brew install -v --HEAD moose-nightly
   - /usr/local/bin/python3 -c "import moose; print(dir(moose))"
   - set +e
+  - /usr/local/bin/python3 -m pip install matplotlib scipy networkx
+  - /usr/local/bin/python3 -c "import moose;moose.test()"

From a677ab39fc5f22c80ad46d44b0211d044de5d791 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Sat, 1 Feb 2020 20:37:44 +0530
Subject: [PATCH 20/21] Create main.yml

---
 .github/workflows/main.yml | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 .github/workflows/main.yml

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
new file mode 100644
index 0000000..e50273c
--- /dev/null
+++ b/.github/workflows/main.yml
@@ -0,0 +1,2 @@
+- name: GitHub Action for Homebrew
+  uses: artemnovichkov/action-homebrew@0.1.0

From 0cf8b85ee0e4a47bae359924c07708d7b443648c Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Fri, 13 Mar 2020 21:17:46 +0530
Subject: [PATCH 21/21] Update moose-nightly.rb

Official URL.
---
 moose-nightly.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/moose-nightly.rb b/moose-nightly.rb
index e999f75..fe66026 100644
--- a/moose-nightly.rb
+++ b/moose-nightly.rb
@@ -2,7 +2,7 @@ class MooseNightly < Formula
   desc "Multiscale Object Oriented Simulation Environment"
   homepage "http://moose.ncbs.res.in"
   version "3.2-nightly"
-  head "https://github.com/dilawar/moose-core.git", :branch => "master"
+  head "https://github.com/BhallaLab/moose-core.git", :branch => "master"
 
   depends_on "cmake" => :build
   depends_on "gsl"